Quickstart¶
Installation¶
SASS is both a standalone application and a Fiji plugin.
Standalone¶
- Download the latest .jar file from the SASS releases page.
- You will also need to download the latest ALICA_ACPack .jar, which contains the run-time components for control systems simulations.
- Place both .jars in the folder of your choosing.
Fiji¶
- Download the latest .jar file from the SASS releases page.
- You will also need to download the latest ALICA_ACPack .jar, which contains the run-time components for control systems simulations.
- Copy the SASS .jar file into your ~/Fiji.app/plugins/ folder, where Fiji.app is root directory for your Fiji installation.
- Copy the ALICA_ACPack .jar file into your ~/Fiji.app/jars folder.
- Restart Fiji.
You should now see SASS appear as a menu item in the the Plugins menu.
Run a simulation¶
Standalone¶
Before starting, make sure that you have a copy of the file example_random_2d_fluorophores.bsh from the SASS respository’s scripts folder. When using SASS in standalone mode, it is most commonly used as a command line application.
- From the command line, navigate to the folder where you placed the SASS .jar file that you downloaded in the installation step.
- Enter the command java -jar SASS_-<VERSION>.jar -s example_random_2d_fluorophores.bsh.
- If you want to save the simulation’s output, ensure that any call to the saveStack(…) method is uncommented inside the script and rerun the simulation.
Fiji¶
- Launch Fiji. (If you’re launch Fiji from the command line, ensure that you are first in the Fiji root directory.)
- Navigate to Plugins > SASS > Simulator.
- Ensure that Manual is selected in the Controller drop-down box.
- Click the Initialize button.
- Rearrange the windows so that you can find the dialog with the controller set point and the Start and Stop buttons.
- Click Start to start the simulation. You should see images begin streaming into the simulation’s image stack.
- Click the Stop button to pause the simulation.
- Change the Controller setpoint value and click Start again to resume the simulation with a new laser power.